In this work, a detailed analysis of the properties of a novel microdosimeter based on a synthetic single crystal diamond is reported. Focused ion microbeams were used to investigate the device spectropscopic properties as well as the induced radiation damage effects. A diamond based Schottky diode was fabricated by chemical vapor deposition with a very thin detecting region, about 400 nm thick (approximately 1.4 μm water equivalent thickness), corresponding to the typical size in microdosimetric measurements. A 200 × 200 μm2 square metallic contact was patterned on the diamond surface by standard photolithography to define the sensitive area. Experimental measurements were carried out at the Ruder Boškovic′ Institute microbeam facility using 4 MeV carbon and 5 MeV silicon ions. Ion beam induced charge maps were employed to characterize the microdosimeter response in terms of its charge collection properties. A stable response with no evidence of polarization or memory effects was observed up to the maximum investigated ion beam flux of about 1.7 × 109 ions·cm−2·s−1. A homogeneity of the response about 6% was found over the sensitive region with a well-defined confinement of the response within the active area. Tests of the radiation damage effect were performed by selectively irradiating small areas of the device with different ion fluences, up to about 1012 ions/cm2. An exponential decrease of the charge collection efficiency was observed with a characteristic decay constant of about 4.8 MGy and 1 MGy for C and Si ions, respectively. The experimental data were analyzed by means of GEANT4 Monte Carlo simulations. A direct correlation between the diamond damaging effect and the Non Ionizing Energy Loss (NIEL) fraction was found. In particular, an exponential decay of the charge collection efficiency with an exponential decay as a function of NIEL is observed, with a characteristic constant of about 9.3 kGy-NIEL for both carbon and silicon ions.